The purpose of this paper is to present a summary of the application of non-destructive techniques used in a comparative study of eighty pottery fragments of the Chalcolithic period (5000 BC ca.) and Late Bronze Age (1650 - 1200 BC ca.), found in Mersin-Yumuktepe (Southern Turkey) and Arslantepe (Malatya, Eastern Turkey). The use of a scanning electron microscopy, equipped with a system of energy dispersive X-ray spectroscopy (SEM-EDX), has allowed determining their morphology, the main inclusions and the elemental composition of ceramic mixtures of each artifact. Moreover, the determination of majority and trace elements has revealed various information, such as the origin of raw materials or the contamination that occurred in the manufacturing phase. The multivariate statistical method has allowed highlighting similarities and/or differences among the ceramics.